Exam in R for data science - Group 12

Breast Cancer Response Analysis

Group 12:

Sofie Emilie Hagelund • Henrique Gomes • Paula Meerjanssen • Shuyue Zhang • Eszter Hudra

Chosen dataset:

MAQC-II Project: human breast cancer (BR) dataset

Dataset Overview

• Demographics: Age, Race
• Clinical (in Grades):
  • Tumor Size before Treatment
  • Lymph node involvement before Treatment
  • Grade/Level of Aggressiveness
• Receptor Status(+/-):
  • Estrogen Receptor
  • Progesterone Receptor
  • HER2 Receptor
• Treatments
• Response to Treatment:
  • pCR = pathological complete response (=good)
  • RD = residual disease (=bad)

Demographics - Age and Race

- Breast cancer patients are mainly white and between the ages of 40-59.

Age and Genotype

• The most common Genotype trend is
  • ER+, PR+, HER2-
  • ER-, PR-, HER2- (Triple negative)

There is no clear correlation between age and genotype.

Do the theoretically predicted prognoses for the genotypes match the observed responses in the dataset?

ER+ patients have the worst treatment response

• Surprisingly:
  • ER+ patients have the worst treatment response.
  • HER2+ only patients and triple-negative patients have the best treatment response.

Does the treatment response from the genotypes correlate with tumor aggressiveness, size, and lymph node involvement?

Treatment response does not correlate with tumor aggressiveness

• ER+ do not have a more aggressive tumor grade = no correlation to response.
• ER-, PR- have a more aggressive tumor grade = no correlation to response.

Does the treatment response from the genotypes correlate with tumor aggressiveness, size, and lymph node involvement?

Treatment response does not correlate with tumor size

• Most of the genotypes have a tumor size of 2, or developed into size 3-4. Especially the case for:

  • ER+ genotype, and ER-, PR- genotype combinations.

Does the treatment response from the genotypes correlate with tumor aggressiveness, size, and lymph node involvement?

Treatment response does not correlate with lymph node involvement

• Generally, following genotypes have the most lymph node involvement:

  • ER+, PR-, HER2-

  • ER-,PR-, HER2+

  • ER-, PR-, HER2- (triple negative)

Does the response and treatment type give any insights into whether a specific treatment is favorable for certain genotypes?

More treatment options lead to better response

• The last two groups were exposed to the most different treatment options:

  • ER-,PR-, HER2+ and ER-, PR-, HER2- (triple negative)

• A general broad TFAC and TFEC is not working for ER+ patients.

Conclusion

• More personalized treatment options give better response.
  
  

• The level of aggressiveness, tumor size, and lymph node involvement do not necessarily mean a bad response if personalized treatment is an option.

Reference

Shi L. Gene expression data from 230 stage I–III breast cancers (GSE20194). NCBI Gene Expression Omnibus. GEO Series GSE20194. Accessed via https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20194